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Diatoms are a successful group of marine phytoplankton that often thrives under adverse environmental stress conditions. Members of the <i>Skeletonema</i> genus are ecologically important which may subsist during silicate stress and form a dense bloom following higher silicate concentration. However, our understanding of diatoms&#8217; underlying molecular mechanism involved in these intracellular silicate stress-responses are limited. Here an iTRAQ-based proteomic method was coupled with multiple physiological techniques to explore distinct cellular responses associated with oxidative stress in the diatom <i>Skeletonema dohrnii</i> to the silicate limitation. In total, 1768 proteins were detected; 594 proteins were identified as differentially expressed (greater than a two-fold change; <i>p</i> &lt; 0.05). In Si-limited cells, downregulated proteins were mainly related to photosynthesis metabolism, light-harvesting complex, and oxidative phosphorylation, corresponding to inducing oxidative stress, and ROS accumulation. None of these responses were identified in Si-limited cells; in comparing with other literature, Si-stress cells showed that ATP-limited diatoms are unable to rely on photosynthesis, which will break down and reshuffle carbon metabolism to compensate for photosynthetic carbon fixation losses. Our findings have a good correlation with earlier reports and provides a new molecular level insight into the systematic intracellular responses employed by diatoms in response to silicate stress in the marine environment.